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- PDB-4woz: Crystal Structures of CdNal from Clostridium difficile in complex... -

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Basic information

Entry
Database: PDB / ID: 4woz
TitleCrystal Structures of CdNal from Clostridium difficile in complex with mannosamine
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / aldolase / thermostable
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytoplasm
Similarity search - Function
N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...N-acetylneuraminate lyase / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-(ACETYLAMINO)-2-DEOXY-D-MANNOSE / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLiu, W.D. / Guo, R.T. / Cui, Y.F. / Chen, X. / Wu, Q.Q. / Zhu, D.M.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China21072151 China
National Natural Science Foundation of China21102100 China
National Basic Research Program of China2011CB710801 China
CitationJournal: to be published
Title: Crystal Structures of CdNal from Clostridium difficile in complex with mannosamine
Authors: Liu, W.D. / Guo, R.T. / Cui, Y.F. / Chen, X. / Wu, Q.Q. / Zhu, D.M.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
E: N-acetylneuraminate lyase
F: N-acetylneuraminate lyase
G: N-acetylneuraminate lyase
H: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,39810
Polymers274,9568
Non-polymers4422
Water36,4082021
1
A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
C: N-acetylneuraminate lyase
E: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6995
Polymers137,4784
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-60 kcal/mol
Surface area39360 Å2
MethodPISA
2
D: N-acetylneuraminate lyase
F: N-acetylneuraminate lyase
G: N-acetylneuraminate lyase
H: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6995
Polymers137,4784
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-58 kcal/mol
Surface area39600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.476, 121.604, 121.065
Angle α, β, γ (deg.)90.000, 96.120, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein
N-acetylneuraminate lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid ...N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid aldolase / Sialic acid lyase


Mass: 34369.492 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: NAP08 / Gene: nanA, CdNal / Plasmid: pET32 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5Q364, N-acetylneuraminate lyase
#2: Chemical ChemComp-MN9 / 2-(ACETYLAMINO)-2-DEOXY-D-MANNOSE


Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2021 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: NaAc, PEG 8000, ketonebutyric,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 169123 / % possible obs: 99.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Χ2: 0.966 / Net I/av σ(I): 19.455 / Net I/σ(I): 8.3 / Num. measured all: 557843
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.023.20.515167320.810.3450.6220.70899
2.02-2.13.30.382169110.8790.2530.460.73599.9
2.1-2.23.30.277169480.9280.1820.3330.767100
2.2-2.313.30.198169220.9640.130.2380.798100
2.31-2.463.30.152169110.9760.10.1830.838100
2.46-2.653.30.114169230.9860.0750.1370.862100
2.65-2.913.30.079169830.9920.0520.0950.88699.9
2.91-3.333.30.054169330.9960.0350.0650.98799.8
3.33-4.23.30.047169340.9960.030.0571.80299.4
4.2-253.30.03169260.9980.020.0361.27198.4

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Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F74

1f74


Resolution: 1.96→25 Å / FOM work R set: 0.8277 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 7920 4.7 %Random selection
Rwork0.1882 149939 --
obs-157859 94.1 %-
Solvent computationBsol: 77.5483 Å2
Displacement parametersBiso max: 100.19 Å2 / Biso mean: 36.2744 Å2 / Biso min: 16.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.154 Å2-0 Å212.859 Å2
2---0.146 Å2-0 Å2
3---1.3 Å2
Refinement stepCycle: final / Resolution: 1.96→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18561 0 30 2021 20612
Biso mean--92.34 51 -
Num. residues----2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3351.5
X-RAY DIFFRACTIONc_scbond_it2.1582
X-RAY DIFFRACTIONc_mcangle_it2.0132
X-RAY DIFFRACTIONc_scangle_it3.1932.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3MN9.par

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